Marcel Amills, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB)
One of the most significant advances in the field of caprine genomics was the genome sequencing of a 3-year-old female Yunnan black goat in 2013 by a Chinese team led by Dr. Wen Wang. The aim was achieved by smartly combining conventional next generation short-read sequencing with an optical mapping technology that facilitated the laborious process of genome assembly.
On March 2017, Dereck Bickhart and colleagues published in Nature Genetics a refined and more accurate version of the goat genome, where many existing gaps were filled, thus yielding one of the most continuous de novo mammalian assemblies generated to date. This refined goat genome was produced by using, once again, short-read next generation sequencing and optical mapping plus two additional techniques: chromosome interaction mapping and single-molecule long-read sequencing performed in a Pacific Biosciences PacBio RSII platform. By merging the information produced with these four complementary tools, researchers were able to obtain a final 2.92 Gb assembly which represents a significant improvement of previous genome versions, particularly on repetitive and highly polymorphic regions that, in general, are difficult to assemble.
Having an accurate goat reference genome at hand is central to many genetic applications. For instance, genome-wide association studies and selection scans aiming to uncover the genetic basis of quantitative traits rely on the precise mapping of genetic markers to the reference genome. The role of structural variation on goat phenotypes can be only investigated if a highly-refined genome is available. For all these reasons, the study published by Bickhart and colleagues can be anticipated to boost genetic research on goats.
A positive impact, for instance, is expected on the VarGoats project (http://www.goatgenome.org/vargoats.html) led by Dr. Gwenola Tosser-Klopp from INRA and supported by France Genomique (https://www.france-genomique.org). The goal of this project is to provide an unprecedented view of goat genetic variation by sequencing the genomes of more than 500 goats with a worldwide distribution. Millions of polymorphisms will be identified in this way, making it possible to ascertain genetic relationships amongst caprine breeds as well to trace their origins and demographic histories with extraordinary accuracy.
In brief, goat genomics has made a giant leap in less than five years and the pace at which discoveries are made ensures that many unknown biological features of this domestic species will be soon uncovered.
Dong et al. (2013) Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat. Biotechnol. 31: 135-41.
Bickhart et al. (2017) Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat. Genet. 49:643-650.
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